In a culture where silence is golden and spoken words can be vague or meaningless, body language is very important.
Japan is a society that uses high-context communication, meaning that contextual factors play a prominent role (as opposed to most European cultures which are low context). The TV news in Japan spends a great deal of time analyzing facial expressions and eye movements rather than focusing on a person's words. For this reason, mastering Japanese body language is just as important as the actual spoken language.
The basics of not offending or frightening people
In Japan, eye contact equals aggression. If you look someone in the eye, they look away. Direct eye contact is considered rude or intrusive. It's alright to make brief eye contact, but for the bulk of the conversation you should look somewhere else. If you're a person dumbfounded by the standoffishness of the Japanese you meet, it could be because they think you're staring them down.
Posture is extremely important. Good posture tells the other person that you're respectful and attentive. It's bad to sit slumped over like a teenager at McDonalds and people don't usually lean casually against walls. Sitting with arms or legs outspread is a serious sin in Japan – you're taking up space. This causes irritation but it's also a sign of confidence, which many Japanese interpret as over-confidence or arrogance.
Don't point. Even if indicating an inanimate object, Japanese people use the open hand as if leading the way toward it. The open hand gesture should be done gently so it doesn't feel like you're jabbing at someone.
Counting backwards and beckoning someone to go away
Japanese hand gestures can cause a bit of confusion. Perhaps the most common one is the 'come here,' which looks like 'go away' to foreign folk. You let your wrist go limp and flap your fingers at the person. This is what the maneki-neko (招き猫 – beckoning cat) you see in stores is doing when it looks like it's waving goodbye to you. This is a useful hand gesture to know, but don't use it with superiors.
Counting is also maddeningly confusing. In Japan, you start number one by folding your thumb into your open hand. The index finger comes next, then the middle finger, and so on until you've got a fist. From 6, you start unfolding your fingers starting with the pinky. If you live in Japan long enough, you'll start doing this subconsciously and confuse the heck out of everyone when you go home to visit.
Have you ever seen someone make devil horns? No, they're not getting carried away at a Black Sabbath concert. This indicates anger. You put the index fingers at both sides of the top of the head and point up. It looks like the horns of an oni (鬼 - devil).
Other common hand gestures include the 'okay' sign, which means money. This is usually used by males and isn't considered polite. Another is the ubiquitous peace sign, which is used when posing for snapshots especially if you're a high school girl.
Looking at your shoes
No mention of Japanese body language is complete without the bow. Bowing in Japan shows respect toward the other person. For men, you put your hands on the sides of your legs. Women commonly place their palms flat on the front of their legs. Then, you lower your head so that the other person can give you a comical slap if they want to.
The depth and length of time of the bow depends on the situation and social rank of each person. For a regular bow, take a second to look at the other person's shoes. If you really want to show respect, examine your own shoes for a minute. Friends casually acknowledge each other or say thinks with a smile and quick head nod.
Saying what's not said
In Japan, silence is golden. It's a part of the conversation and can mean agreement, disagreement, shock, defiance, stubbornness, shyness… and practically any other human emotion. It's the go-to whenever someone is troubled. It's there for you when you don't have anything particular to say. Don't stress if you find gaps in the jawing.
Finally, if a member of the opposite sex pulls out an English textbook and starts 'studying' next to you on the train, this means, 'Hi, how are you and where are you from?'